Shotgun proteomics experiments use surfactants to achieve efficient extraction and digestion of proteins. The surfactants widely used in shotgun proteomics can be classified as ionic (e.g., sodium dodecyl sulfate (SDS)), nonionic (e.g., Triton-X), and acid cleavable surfactants (e.g., RapiGest). A typical strategy for shotgun proteomics of samples containing membrane proteins begins with protein extraction from cells or tissues in the presence of a surfactant, then cystine residues are reduced and alkylated under denaturing conditions, and then the surfactant is subsequently removed by acetone precipitation or by exchange with urea on a standard filtration device. The resulting acetone precipitate is generally solubilized either in a strong chaotropic agent, such as urea or guanidine hydrochloride (Gdn-HCl) or in a surfactant, and then subjected to proteolytic digestion. After the digestion, the chaotropic agent are removed by a reverse-phase solid phase extraction. However, when a surfactant is used, it cannot be removed easily from the digest. Because surfactants are hydrophobic in nature, they cause peak broadening and suppress the ionization of peptides in the subsequent LC-MS/MS analysis. Thus, the surfactants used must be removed prior to LC-MS/MS analysis.
Surfactants can be removed from peptide mixtures either by ion exchange chromatography, by phase transfer, or by washing with chlorinated solvents while peptides are captured on a reversed phase cartridge. These extra preparation steps have the major drawback of losing peptides to the stationary phase during the procedures, which cannot be afforded when sample amount is limited. To avoid this problem, acid labile surfactants have been developed that can be cleaved between the hydrophobic and hydrophilic part of the surfactants after the protein digestion. The hydrophobic part precipitates upon the acid cleavage, allowing its removal from the digest. The hydrophilic part does not interfere with the subsequent LC-MS/MS analysis. However, it has been reported that hydrophobic peptides are lost from the digest due to their interactions with the precipitated hydrophobic part of the surfactant. Thus, a method is needed that does not lead to the loss of peptides.